Regressor file not found - fmriDenoise

orduek · September 4, 2019, 6:28pm

Hi,
Just tried to run one subject in fmridenoise - I get this error:

fmridenoise /media/Data/KPE_fmriPrep_preproc/kpeOutput -sub 1253 -ses 1 -t rest
/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/site-packages/sklearn/externals/joblib/init.py:15: DeprecationWarning: sklearn.externals.joblib is deprecated in 0.21 and will be removed in 0.23. Please import this functionality directly from joblib, which can be installed with: pip install joblib. If this warning is raised when loading pickled models, you may need to re-serialize those models with scikit-learn 0.21+.
warnings.warn(msg, category=DeprecationWarning)
190904-14:23:34,402 nipype.workflow INFO:
Workflow fmridenoise_wf settings: [‘check’, ‘execution’, ‘logging’, ‘monitoring’]
190904-14:23:34,435 nipype.workflow INFO:
Running serially.
190904-14:23:34,435 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path..home..or..miniconda3..envs..neuroAnalysis..lib..python3.7..site-packages..fmridenoise..pipelines..pipeline-24HMP_aCompCor_SpikeReg.json/PipelineSelector”.
190904-14:23:34,436 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190904-14:23:34,437 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190904-14:23:34,437 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path..home..or..miniconda3..envs..neuroAnalysis..lib..python3.7..site-packages..fmridenoise..pipelines..pipeline-ICA-AROMA_8Phys.json/PipelineSelector”.
190904-14:23:34,437 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190904-14:23:34,437 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190904-14:23:34,437 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path..home..or..miniconda3..envs..neuroAnalysis..lib..python3.7..site-packages..fmridenoise..pipelines..pipeline-24HMP_8Phys_SpikeReg.json/PipelineSelector”.
190904-14:23:34,438 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190904-14:23:34,438 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190904-14:23:34,438 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path..home..or..miniconda3..envs..neuroAnalysis..lib..python3.7..site-packages..fmridenoise..pipelines..pipeline-24HMP_8Phys_SpikeReg_4GS.json/PipelineSelector”.
190904-14:23:34,438 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190904-14:23:34,438 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190904-14:23:34,439 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path..home..or..miniconda3..envs..neuroAnalysis..lib..python3.7..site-packages..fmridenoise..pipelines..pipeline-ICA-AROMA_8Phys_4GS.json/PipelineSelector”.
190904-14:23:34,439 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190904-14:23:34,439 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190904-14:23:34,439 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path..home..or..miniconda3..envs..neuroAnalysis..lib..python3.7..site-packages..fmridenoise..pipelines..pipeline-24HMP_aCompCor_SpikeReg_4GS.json/PipelineSelector”.
190904-14:23:34,440 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190904-14:23:34,440 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190904-14:23:34,440 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.PipelineSelector” in “/tmp/fmridenoise/fmridenoise_wf/pipeline_path..home..or..miniconda3..envs..neuroAnalysis..lib..python3.7..site-packages..fmridenoise..pipelines..pipeline-Null.json/PipelineSelector”.
190904-14:23:34,440 nipype.workflow INFO:
[Node] Cached “fmridenoise_wf.PipelineSelector” - collecting precomputed outputs
190904-14:23:34,440 nipype.workflow INFO:
[Node] “fmridenoise_wf.PipelineSelector” found cached.
190904-14:23:34,441 nipype.workflow INFO:
[Node] Setting-up “fmridenoise_wf.BidsGrabber” in “/tmp/fmridenoise/fmridenoise_wf/BidsGrabber”.
190904-14:23:34,442 nipype.workflow INFO:
[Node] Running “BidsGrabber” (“fmridenoise.interfaces.bids.BIDSGrab”)
190904-14:24:02,274 nipype.workflow WARNING:
[Node] Error on “fmridenoise_wf.BidsGrabber” (/tmp/fmridenoise/fmridenoise_wf/BidsGrabber)
190904-14:24:02,275 nipype.workflow ERROR:
Node BidsGrabber failed to run on host or-ThinkStation-P520.
190904-14:24:02,275 nipype.workflow ERROR:
Saving crash info to /home/or/crash-20190904-142402-or-BidsGrabber-a02bf2f5-5bbe-4b01-a700-a6b951795316.pklz
Traceback (most recent call last):
File “/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py”, line 48, in run
node.run(updatehash=updatehash)
File “/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 472, in run
result = self._run_interface(execute=True)
File “/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 563, in _run_interface
return self._run_command(execute)
File “/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py”, line 643, in _run_command
result = self._interface.run(cwd=outdir)
File “/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/site-packages/nipype/interfaces/base/core.py”, line 375, in run
runtime = self._run_interface(runtime)
File “/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/site-packages/fmridenoise/interfaces/bids.py”, line 277, in _run_interface
f"Regressor file not found for file {fmri_file.path}"
FileNotFoundError: Regressor file not found for file /media/Data/KPE_fmriPrep_preproc/kpeOutput/derivatives/fmriprep/sub-1253/ses-1/func/sub-1253_ses-1_task-rest_space-MNI152NLin2009cAsym_desc-preproc_bold.nii.gz

190904-14:24:02,276 nipype.workflow INFO:

190904-14:24:02,276 nipype.workflow ERROR:
could not run node: fmridenoise_wf.BidsGrabber
190904-14:24:02,276 nipype.workflow INFO:
crashfile: /home/or/crash-20190904-142402-or-BidsGrabber-a02bf2f5-5bbe-4b01-a700-a6b951795316.pklz
190904-14:24:02,276 nipype.workflow INFO:

Traceback (most recent call last):
File “/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/runpy.py”, line 193, in _run_module_as_main
“main”, mod_spec)
File “/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/runpy.py”, line 85, in _run_code
exec(code, run_globals)
File “/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/site-packages/fmridenoise/main.py”, line 168, in
main()
File “/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/site-packages/fmridenoise/main.py”, line 164, in main
workflow.run()
File “/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/site-packages/nipype/pipeline/engine/workflows.py”, line 599, in run
runner.run(execgraph, updatehash=updatehash, config=self.config)
File “/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/site-packages/nipype/pipeline/plugins/linear.py”, line 71, in run
report_nodes_not_run(notrun)
File “/home/or/miniconda3/envs/neuroAnalysis/lib/python3.7/site-packages/nipype/pipeline/plugins/tools.py”, line 82, in report_nodes_not_run
raise RuntimeError(('Workflow did not execute cleanly. ’
RuntimeError: Workflow did not execute cleanly. Check log for details

When looking at ses-1 of 1253, I do have both functional and regressor file (its name is: sub-1253_ses-1_task-rest_desc-confounds_regressors.tsv)

Any ideas?

Jhig · September 6, 2019, 12:10am

Having same issue, haven’t found solution yet

ncross · September 8, 2019, 5:52pm

It looks like the workflow is trying to look for a _regressors.json file also, which is not a current output of fmriprep (at least I don’t think so).

Is there a particular reason this toolbox requires both .tsv and .json formats to run?